6UML: DNA damage-binding protein 1

Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex. Determined by X-ray diffraction at 3.58 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 3.58 Å
Organism: Homo sapiens
Chains: 3
Atoms: 11,104
Mol. weight: 177.36 kDa
Ligands: ZN, Y70
Released: 15 Apr 2020

Explore 6UML in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UML contains 29 α-helices and 128 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 106 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
β-strand	17-21	5	2
β-strand	30-34	5	2
β-strand	39-43	5	2
β-strand	50-55	6	2
β-strand	61-67	7	3
β-strand	76-81	6	3
β-strand	85-92	8	3
β-strand	99-107	9	3
α-helix	114	1
β-strand	115	1	4
α-helix	116	1
β-strand	121-124	4	5
β-strand	130-134	5	5
β-strand	136	1	4
β-strand	139-144	6	5
β-strand	155-158	4	5
β-strand	164-169	6	6
α-helix	170	1
β-strand	177-184	8	6
β-strand	187-195	9	6
β-strand	202-209	8	6
β-strand	218-221	4	7
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	251-253	3
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-290	12	8
β-strand	293-307	15	8
β-strand	311-317	7	9
β-strand	321-326	6	9
β-strand	331-337	7	9
α-helix	338-339	2
β-strand	346-353	8	9
β-strand	361-365	5	10
β-strand	374-379	6	10
α-helix	382-384	3
β-strand	386-393	8	10
β-strand	394	1	11
β-strand	396-403	8	12
β-strand	409-413	5	13
β-strand	422	1	14
β-strand	424-429	6	13
β-strand	432-439	8	13
β-strand	442-446	5	13
β-strand	457-463	7	15
β-strand	467-472	6	15
β-strand	476-480	5	15
β-strand	486-490	5	15
α-helix	496-498	3
β-strand	500	1	16
β-strand	503	1	16
β-strand	507-512	6	16
β-strand	515-522	8	16
β-strand	525-532	8	16
β-strand	538-542	5	17
β-strand	555-560	6	17
β-strand	565-570	6	17
β-strand	579-581	3	17
β-strand	588-595	8	18
β-strand	600-606	7	18
β-strand	610-614	5	18
β-strand	615-616	2	19
β-strand	623-624	2	19
β-strand	628-630	3	18
β-strand	637-643	7	20
β-strand	646-652	7	20
β-strand	653	1	21
β-strand	657-661	5	20
β-strand	666-670	5	20
β-strand	671	1	11
β-strand	676	1	21
β-strand	678-682	5	12
β-strand	684	1	14
β-strand	690-694	5	12
β-strand	698-704	7	12
β-strand	709-716	8	10
β-strand	720-727	8	22
β-strand	732-742	11	22
β-strand	750-751	2	22
β-strand	762-765	4	22
β-strand	786-795	10	22
β-strand	801-806	6	22
β-strand	811-819	9	23
β-strand	828-835	8	23
β-strand	846	1	24
β-strand	848-854	7	23
β-strand	857-862	6	23
β-strand	866	1	24
β-strand	873-876	4	25
β-strand	879-884	6	25
β-strand	887-893	7	25
β-strand	899-906	8	25
β-strand	913-917	5	26
β-strand	920-924	5	26
β-strand	930-936	7	26
α-helix	937-939	3
β-strand	941-948	8	26
β-strand	954-959	6	27
β-strand	964-969	6	27
β-strand	973-978	6	27
β-strand	991	1	26
β-strand	993-999	7	27
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1043	7	1
α-helix	1045-1061	17
α-helix	1070-1074	5
β-strand	1076-1077	2	28
β-strand	1082-1083	2	28
β-strand	1086	1	27
β-strand	1090	1	1
α-helix	1091-1094	4
α-helix	1095-1098	4
α-helix	1102-1108	7
β-strand	1113	1	29
β-strand	1123	1	29
α-helix	1126-1136	11

Chain C: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
α-helix	73-74	2
β-strand	78-81	4	30
β-strand	83	1	31
β-strand	96-101	6	31
α-helix	104-113	10
β-strand	119-122	4	31
β-strand	136-149	14	31
β-strand	152-165	14	31
β-strand	180-183	4	30
β-strand	184	1	31
α-helix	185-186	2
β-strand	188	1	32
α-helix	200-203	4
α-helix	222-231	10
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-263	14
α-helix	277-287	11
α-helix	292-300	9
β-strand	303	1	32
α-helix	304-317	14
β-strand	320-323	4	33
β-strand	330-333	4	33
α-helix	334-336	3
β-strand	337	1	34
β-strand	346-350	5	34
β-strand	356-362	7	34
β-strand	368-375	8	34
β-strand	384-391	8	34
β-strand	397-404	8	34
β-strand	413-418	6	34
α-helix	419-421	3
β-strand	422-425	4	33

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	410-411	2	35
β-strand	418-419	2	35
α-helix	422-429	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	C	protein	406	Homo sapiens	Q96SW2 (AlphaFold model)
Sal-like protein 4	E	protein	28	Homo sapiens	Q9UJQ4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6UML_1 DNA damage-binding protein 1 (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (C), FASTA

>6UML_2 Protein cereblon (chains C)
GSMEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQT
LPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVK
VKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSRE
DQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSN
PIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNE
IFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICAS
HIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Sequence of entity 3 (E), FASTA

>6UML_3 Sal-like protein 4 (chains E)
TGERPFVCSVCGHRFTTKGNLKVHFHRH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
Y70	S-Pomalidomide	C13 H11 N3 O4	1

Primary citation

Crystal structure of the SALL4-pomalidomide-cereblon-DDB1 complex. Matyskiela, M.E., Clayton, T., Zheng, X. et al. Nat Struct Mol Biol (2020) 27:319-322. DOI 10.1038/s41594-020-0405-9 · PubMed

Other PDB entries of the same protein (UniProt Q16531 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BBG 1.7 Å, Co-crystal structure of human DDB1 bound to fragment UB028671
9EJQ 1.87 Å, Crystal structure of DDB1 in complex with XS381952
9BBI 1.9 Å, Co-crystal structure of human DDB1 bound to fragment UB028669
9BZ0 1.9 Å, Structure of an STK19-containing TC-NER complex
9BBE 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028668
9BBH 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028670
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
9ZXN 2.07 Å, DDB1 delta with compound 26
37MF 2.1 Å, Crystal structure of DDB1 in complex with XS445479
9ZXM 2.19 Å, DDB1 delta with compound 6
8G46 2.2 Å, Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2
8ZSW 2.25 Å, Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex

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